Watersheds are increasingly understood as socio-ecological systems (SES), reflecting the close interaction between ecological processes and human activities. However, research trends, thematic developments, and knowledge gaps in watershed-based SES studies have yet to be comprehensively synthesized. This study aims to examine the evolution of SES research in watershed contexts through a systematic review of the scientific literature published between 1999 and 2025. Following the PRISMA approach, records were retrieved from Scopus and Web of Science. A total of 689 documents were initially identified; 455 remained after duplicate removal, and 96 articles met the final eligibility criteria for analysis. The review reveals a substantial increase in watershed-SES publications after 2018. Earlier studies primarily focused on conceptual development, whereas more recent research has expanded toward governance, climate adaptation, resilience, land-use pressures, and agricultural–water interactions. Geographic patterns indicate that studies conducted in the Global North tend to emphasize institutional and modeling approaches, while research in the Global South more frequently addresses socio-ecological pressures and local environmental challenges. The synthesis also highlights the growing use of spatial analytical tools, particularly Geographic Information Systems (GIS) and remote sensing, to investigate watershed dynamics and support management decisions. Based on the findings, this study proposes a conceptual Dynamic SES–Watershed Framework that links ecological thresholds, governance processes, adaptive capacity, resilience, and land-use pressures within watershed systems. However, as a review-based study, the framework is intended as a conceptual foundation for future empirical testing rather than a validated model. The findings contribute to a broader understanding of watershed sustainability and provide directions for future SES research and management.